5N6V | pdb_00005n6v

Crystal structure of Neisseria polysaccharea amylosucrase mutant derived from Neutral genetic Drift-based engineering

• PDB DOI: https://doi.org/10.2210/pdb5N6V/pdb

• Classification: HYDROLASE
• Organism(s): Neisseria polysaccharea
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-02-16 Released: 2018-03-07 
• Deposition Author(s): Daude, D., Verges, A., Tranier, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Neutral Genetic Drift-Based Engineering of a Sucrose-Utilizing Enzyme toward Glycodiversification.

Daude, D., Verges, A., Cambon, E., Emond, S., Tranier, S., Andre, I., Remaud-Simeon, M.

(2019) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.8b03609

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.59 kDa 
• Atom Count: 6,430 
• Modeled Residue Count: 628 
• Deposited Residue Count: 628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amylosucrase	A	628	Neisseria polysaccharea	Mutation(s): 4  Gene Names: ams EC: 2.4.1.4
UniProt
Find proteins for Q9ZEU2 (Neisseria polysaccharea) Explore Q9ZEU2  Go to UniProtKB:  Q9ZEU2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B, C	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
1PE	J [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
GLC	E [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
FRU	H [auth A], I [auth A]	beta-D-fructofuranose C6 H12 O6 RFSUNEUAIZKAJO-ARQDHWQXSA-N
PGE	G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	B, C	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.1	α = 90
b = 96.15	β = 90
c = 116.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Daude, D., Verges, A., Tranier, S.

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2019-03-20
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary